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. 2019 Dec 16;19:553. doi: 10.1186/s12870-019-2015-4

Table 5.

GWAS results for FEh, TGW, GNS, HD and PH. Information of haplotypes/SNPs physical location, frequency in the collection and effect direction, P values in each environment and the colocated traits

Ref. Seq. v1.0 (Mb) Freq. Azul Balcarce Marcos Juárez
Trait Haplotype/SNP1 Chr. Start End Effect2 133 14 13 14 15 11 12 13 14 15 16 Coloc.
FEh Chr1A-B32-Hap4 1A 482.3 487.0 6+ * ns * * ** - ns ns ns ns ns
Chr2A-B19-Hap3 2A 70.2 72.9 12+ * ns * * ns - ** ns * ns ns
Chr2A-B23-Hap1 2A 83.8 84.5 52- * * * * ns - * ns ns * *
Chr2A-B26-Hap3 2A 102.0 102.7 36+ * ** ** * ns - ns ns ns ns *
Chr2A-B30-Hap4 2A 165.8 182.1 7+ ** ns * * ns - ns * ns ns ns
Chr2A-B49-Hap2 2A 704.8 705.8 15+ * * * ** * - ns ns ns ns ns GNS
AX-94874921 2A 707.1 - 16+ ns ns ns ns ns - ** ns * * *
Chr2A-B55-Hap1 2A 716.8 718.9 12+ * *** ** * * - ns ns ns ns ns
Chr3B-B14-Hap4 3B 23.0 24.0 6+ ns ns ** * * - ** ns ns * ns
AX-94869767 4A 606.4 - 18+ * ns * * ns - * * ns * *
Chr4A-B35-Hap3 4A 625.7 625.9 23+ ** * ** * * - ns ns ns ns ns
Chr5A-B33-Hap4 5A 445.2 445.2 7+ ** * * * ns - ns ns ns ns ns PH
Chr5A-B43-Hap1 5A 476.4 476.7 15+ * ns * * ns - ns ** ns * ns
Chr6A-B24-Hap2 6A 205.1 233.3 17+ *** * * ns ns - ns ns ns ns * TGW
Chr6A-B28-Hap4 6A 448.7 454.6 9- * * * ** * - * ns ns ns ns
Chr6A-B29-Hap2 6A 455.6 467.0 25+ *** ns * * ns - ns ns * ns *
Chr7A-B36-Hap2 7A 119.0 126.0 10+ * ns * ** * - ns ns ns ns *
TGW Chr2D-B5-Hap3 2D 17.6 18.2 7- * * ns ns ns - ns ns * * **
Chr3A-B12-Hap3 3A 46.7 52.6 5- ns * ns * * - ** * * ns ns
AX-95257035 3A 686.8 - 11+ ns ns ns ns ns - * ns *** ** *
Chr3B-B111-Hap4 3B 817.4 817.8 11+ ns ns ns * ns - ** ns * * ns PH
AX-94459169 6A 0.6 - 30+ ns ** * ns ns - ns * *** *** **
Chr6A-B20-Hap3 6A 63.8 74.0 21- ns ns * ns ns - ns ns * ** *
Chr6A-B21-Hap3 6A 74.5 101.3 20- ns ns * ns ns - ns ns * ** *
Chr6A-B24-Hap2 6A 205.1 233.3 17- ns ns ** ns ns - * ns * *** * FEh
Chr7B-B38-Hap3 7B 626.1 627.6 5+ ns *** ** ns ns - ns * * ns **
Chr7B-B60-Hap2 7B 702.3 703.7 27+ ns ns ns * ns - * * ** * *
Chr7B-B60-Hap3 7B 702.3 703.7 15+ ns ns * ns ns - * * ** ** **
GNS Chr2A-B49-Hap2 2A 704.8 705.8 15+ * ns * ** ** - ns ns * ns ns FEh
Chr4A-B19-Hap5 4A 231.0 349.3 13+ * ** ns ns ns - ** * * ns *
HD Chr1B-B76-Hap2 1B 643.1 645.7 35+ * ** ns ns ns ** * * ns * *
Chr1B-B84-Hap3 1B 667.2 667.8 17- ns ns ** ** * ns * * * ns ns
Chr1B-B89-Hap4 1B 676.8 678.0 6- ns ns * ** * * * ns * * ns
Chr2B-B40-Hap4 2B 162.9 166.9 10+ * ** ns ns ns ns * ns * * ns
Chr2B-B62-Hap1 2B 564.2 569.0 10+ * ** ns ns ns * ns ns ns * ns
Ppd-D1 sensitive 2D 34 - 42+ * * * * * ** *** ** *** *** **
Chr3A-B31-Hap1 3A 504.8 507.5 59- ns ns * ns * ** * * * * *
Chr3A-B49-Hap3 3A 631.2 633.1 12- ** ns * * ns * * ns * ** *
Chr3A-B59-Hap3 3A 695.5 695.7 19+ ns * ns ns ns ** * ** * * ns
Chr3A-B60-Hap4 3A 699.4 700.6 10+ ns ** ns ns ns ** * *** ** * ns
Chr3D-B7-Hap1 3D 518.2 560.1 54- * * ns ns ns * * ** * * *
Chr5B-B75-Hap4 5B 597.2 601.4 11- * ns ns ns ns * * ns * ** ns
AX-94610041 6A 13.8 - 46+ * * ** * * ** ns * * * ns
Chr6A-B43-Hap1 6A 591.7 592.5 61- ns ** ns ns ns * * ** * * *
Chr6B-B26-Hap3 6B 157.6 157.8 11+ * ** ns ns ns ns ns ns * * ** PH
Chr7A-B24-Hap2 7A 68.0 70.2 8+ ns ns * ** * * ns ** * * ns
PH Chr1A-B38-Hap3 1A 508.6 510.4 16+ * ** ns ns ns * ns ns * ns ns
Chr1B-B17-Hap4 1B 121.0 124.0 5+ * * * ** * *** * * * * **
AX-94510167 1B 548.7 - 21+ ns * ns ** * ** ns ns * ns ns
Chr1B-B54-Hap1 1B 580.5 581.2 43- * ** ns * * * ns ns *** *** ns
Lr10 1D 8.6 - 10+ * * ** ns * ns * ns * * ns
Chr1D-B5-Hap4 1D 11.6 11.9 19- * ** ns * * * ns * * * *
Chr1D-B10-Hap4 1D 31.1 32.5 10+ * ns *** * ns * * ns ns ns ns
Chr2A-B39-Hap1 2A 611.2 611.9 70- ** ns ** ns ns * ns * ns ns *
Chr2A-B48-Hap3 2A 701.0 702.1 15- * *** * ns * * ns ns * * ns
Chr2B-B56-Hap4 2B 469.2 476.6 6+ ns * ** * ns * ns * ns ** *
Chr2B-B79-Hap3 2B 664.2 664.9 5+ * ns ** * ns ** ns * ns ** *
AX-94687989 2B 702.2 - 52+ ns ** ns ns ns ns * ns ** * ns
Chr2B-B97-Hap1 2B 719.5 719.5 38- ns ** ns ns ns ns * ns ** * *
Chr2B-B114-Hap4 2B 762.0 763.9 8+ ** * * ns * ns ns ns * ns ns
AX-94585596 2B 776.4 - 15+ * ** ns ns * ** * * * ns ns
AX-94624485 2B 776.8 - 10+ * * * ns ns ** * * ns ns ns
Chr2B-B122-Hap3 2B 777.1 777.2 6+ * * * ns * *** ** * * * ns
Chr3A-B22-Hap2 3A 391.5 393.4 53+ * * ns * ns * ** * * ns *
AX-95090222 3A 700.6 - 18+ ** ns ns * ns ns ** ns * ns ns
AX-95083205 3A 743.9 - 46+ ** * ns ns * ns ns * * ns ns
Chr3B-B6-Hap1 3B 16.4 17.1 65- * * * ns * ns * * ** ** *
Chr3B-B55-Hap4 3B 511.1 513.6 6- ** * ns ns * ns ns ns ns * *
Chr3B-B60-Hap6 3B 541.5 544.5 5+ * ns * * ns ** * * * * ns
Chr3B-B109-Hap2 3B 796.0 799.1 9- * ** * ns ns ns ns ns ns * *
Chr3B-B111-Hap4 3B 817.4 817.8 11+ *** ns * * ** *** * ** * * * TGW
Chr4A-B57-Hap6 4A 738.7 739.7 9- * ns ns ** ns ** ns ns ns * ns
Chr4B-B28-Hap5 4B 612.2 613.2 6+ * ** * * * * * * * * ns
Chr4B-B36-Hap2 4B 650.7 650.7 57- ** * * * ns * ** ** ns * ns
Chr5A-B16-Hap4 5A 33.0 33.2 5+ * * * * * ** ** ns ns ns ns
Chr5A-B33-Hap4 5A 445.2 445.2 7- ns *** * ns ns * ns ns ns * * FEh
Chr5A-B54-Hap3 5A 516.1 527.9 5+ ns * * ** ** *** ns ns * * *
Chr5A-B82-Hap2 5A 611.6 613.5 10+ * ns * ns ns * *** ns * ns *
Chr5B-B26-Hap2 5B 430.7 430.7 17+ ** * ns * * * * ns ns ns *
AX-94550178 5B 455.7 - 46+ ns ns *** * * * ns ns * ns ns
Chr5B-B92-Hap4 5B 683.5 684.0 5+ * ns * * ns ** * * * ns **
Chr6A-B2-Hap5 6A 0.6 0.8 5+ * ns ** ** * ns ns ns * * ns
Chr6A-B4-Hap2 6A 2.2 2.7 26+ * ns * * ** ns * ns ns * ns
Chr6A-B4-Hap3 6A 2.2 2.7 17- ** * * ns * ns * ns * ** *
Chr6A-B16-Hap1 6A 48.6 49.8 57+ ns ns ns * ns * * ns ** * **
Chr6A-B17-Hap3 6A 50.3 51.4 33- ns * * * ns ** ns * * ** ns
Chr6A-B54-Hap5 6A 610.0 610.2 6+ ns ns * * ns *** ns ** ns ns ns
Chr6B-B7-Hap2 6B 19.8 20.7 82- ** *** ** * ns * *** * * * *
Chr6B-B20-Hap4 6B 124.4 126.1 6+ * ns ns ns ns ** * * ns * *
Chr6B-B25-Hap4 6B 151.4 156.4 25- * ** * * ** ns ns ns * * ns
Chr6B-B26-Hap3 6B 157.6 157.8 11- * *** ns * ns * * * ns * *** HD
Chr6B-B31-Hap2 6B 195.3 197.8 5+ * ns ** ** * ** ns ns * * *
AX-94943227 6B 234.8 - 17+ ** *** ** * * * *** * * * *
Chr6B-B47-Hap3 6B 480.4 491.6 24- ns ns ns * ** ns ns ns * ns *
AX-94476474 7A 561.6 - 14+ ** * * ns ns ns ns ** * * ns
Chr7B-B14-Hap4 7B 59.6 61.6 22- *** ns ns ns * ns * ns ns * ns
Chr7B-B76-Hap3 7B 743.5 743.6 10- ** *** * * ns * ns * ** ** *

1 Information about SNPs ID and/or gene molecular marker that were involved in the haplotypes was detailed in the Additional file 6: Table S5. 2 Freq. = Number of genotypes that present the SNP / haplotype in the collection. Effect (+) the SNP / haplotype increases the phenotypic value and (-) reduces the phenotypic value. 3 Years after 2000. Only SNPs that passed selection criteria in GWAS are presented in the table. ns = not significant, * P <0.05, ** P <0.001, *** P <0.0001, "–" = not available